Abstract
Low-temperature tolerance during the bud-bursting stage is an important characteristic of direct-seeded rice. The identification of cold-tolerance quantitative trait loci (QTL) in species that can stably tolerate cold environments is crucial for the molecular breeding of rice with such traits. In our study, high-throughput QTL-sequencing analyses were performed in a 460-individual F 2 : 3 mapping population to identify the major QTL genomic regions governing cold tolerance at the bud-bursting (CTBB) stage in rice. A novel major QTL, qCTBB9 , which controls seed survival rate (SR) under low-temperature conditions of 5°C/9 days, was mapped on the 5.40-Mb interval on chromosome 9. Twenty-six non-synonymous single-nucleotide polymorphism (nSNP) markers were designed for the qCTBB9 region based on re-sequencing data and local QTL mapping conducted using traditional linkage analysis. We mapped qCTBB9 to a 483.87-kb region containing 58 annotated genes, among which six predicted genes contained nine nSNP loci. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) analysis revealed that only Os09g0444200 was strongly induced by cold stress. Haplotype analysis further confirmed that the SNP 1,654,225 bp in the Os09g0444200 coding region plays a key role in regulating the cold tolerance of rice. These results suggest that Os09g0444200 is a potential candidate for qCTBB9 . Our results are of great significance to explore the genetic mechanism of rice CTBB and to improve the cold tolerance of rice varieties by marker-assisted selection.
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Claims 6
Claim · model-written summary
The major QTL qCTBB9 controls seed survival rate under low-temperature conditions and maps to a 5.40-Mb interval on chromosome 9.
- Taxon
- rice
Oryza sativae0 - Material
- 460-individual F 2 : 3 mapping populatione1
- Treatment
- low-temperature conditions of 5°C/9 dayse2
- Gene
- qCTBB9e2
- Outcome
- seed survival rate (SR)e2
- Qualifier
- 5.40-Mb interval on chromosome 9e2
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Low-temperature tolerance during the bud-bursting stage is an important characteristic of direct-seeded rice”
e1“high-throughput QTL-sequencing analyses were performed in a 460-individual F 2 : 3 mapping population”
e2“A novel major QTL, qCTBB9 , which controls seed survival rate (SR) under low-temperature conditions of 5°C/9 days, was mapped on the 5.40-Mb interval on chromosome 9”
Claim · model-written summary
qCTBB9 was mapped to a 483.87-kb region containing 58 annotated genes.
- Taxon
- riceOryza sativae0
- Gene
- qCTBB9e3
- Outcome
- region containing 58 annotated genese3
- Value
- 483.87-kbe3
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Low-temperature tolerance during the bud-bursting stage is an important characteristic of direct-seeded rice”
e3“We mapped qCTBB9 to a 483.87-kb region containing 58 annotated genes, among which six predicted genes contained nine nSNP loci”
Claim · model-written summary
Six predicted genes in the qCTBB9 region contained nine nSNP loci.
- Taxon
- riceOryza sativae0
- Gene
- qCTBB9e3
- Outcome
- predicted genes containede3
- Value
- nine nSNP locie3
- Qualifier
- among which six predicted genese3
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Low-temperature tolerance during the bud-bursting stage is an important characteristic of direct-seeded rice”
e3“We mapped qCTBB9 to a 483.87-kb region containing 58 annotated genes, among which six predicted genes contained nine nSNP loci”
Claim · model-written summary
In qRT-PCR analysis only Os09g0444200 was strongly induced by cold stress in rice.
- Taxon
- riceOryza sativae0
- Treatment
- cold stresse4
- Gene
- Os09g0444200e4
- Outcome
- only Os09g0444200 was strongly inducede4
- Direction
- strongly inducede4
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Low-temperature tolerance during the bud-bursting stage is an important characteristic of direct-seeded rice”
e4“Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) analysis revealed that only Os09g0444200 was strongly induced by cold stress”
Claim · model-written summary
Haplotype analysis associated the SNP at 1,654,225 bp in the Os09g0444200 coding region with cold tolerance in rice.
- Taxon
- riceOryza sativae0
- Gene
- Os09g0444200e5
- Outcome
- cold tolerancee5
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Low-temperature tolerance during the bud-bursting stage is an important characteristic of direct-seeded rice”
e5“Haplotype analysis further confirmed that the SNP 1,654,225 bp in the Os09g0444200 coding region plays a key role in regulating the cold tolerance of rice”
Claim · model-written summary
Os09g0444200 is a potential candidate gene for qCTBB9.
- Taxon
- riceOryza sativae0
- Gene
- Os09g0444200e6
- Outcome
- potential candidate for qCTBB9e6
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Low-temperature tolerance during the bud-bursting stage is an important characteristic of direct-seeded rice”
e6“These results suggest that Os09g0444200 is a potential candidate for qCTBB9”